tbuckley/cabot-search huggingface dataset:
<i>JAMA Oncology</i>—The Year in Review, 2022
Authors: Mary L. (Nora) Disis
Journal: JAMA Oncology (2023)

This past year has been an exciting one for JAMA Oncology and its editors.We have had the pleasure of receiving a substantial number of submissions and reviewing a diverse and interesting array of topics.Diversity in the oncology workforce and disparities in health equity were common topics.Articles ranged from data on lack of access to cancer screening for some populations, to the inability to access health technology, to the role of zip code in cancer care.We continued to receive reports about the COVID-19 pandemic in cancer, including studies that explore the efficacy of specific vaccines on the more aggressive variants of the virus and the role of booster immunizations in enhancing immune responses in patients.We have reported results from several large phase 3 randomized clinical trials affecting standard of care as well as exciting and promising results from smaller phase 1 and 2 studies with outstanding correlative science.We hope that you enjoyed reading these articles as much as we enjoyed choosing the best manuscripts for publication.We thank the many authors, reviewers, and readers for the significant contributions made to the journal this past year.The JAMA Oncology editorial board, editors, and I are honored to have the opportunity to serve the oncology community by offering original, innovative, and timely scientific content that has a direct effect on researchers, clinicians, and the patients we serve.The impact factor of 33.01 placed JAMA Oncology as one of the highest-ranking oncology journals.Choosing manuscripts for the journal was rewarding, but challenging.We received a total of 2712 submissions this past year, including 1603 Original Investigations, 289 Brief Reports, 234 Research Letters, 117 Viewpoints, and 85 Reviews and Special Communications.In 2022, we published 382 total manuscripts, including 102 Original Investigations, 33 Viewpoints, and 15 Reviews and Special Communications.I would like to thank these authors for choosing JAMA Oncology.The quality of their published manuscripts is reflected in the more than 4 million readers who have viewed or downloaded JAMA Oncology articles.In 2022, the acceptance rates were 14% for overall submissions and 8% for Original Investigations and Brief Reports, 16% for Research Letters, 25% for Review articles, 29% for Viewpoints, and 12% for Clinical Challenges.
A new method for near real-time, nationwide surveillance of nosocomial COVID-19 in Norway: providing data at all levels of the healthcare system, March 2020 to March 2022
Authors: Håvard Skagseth, Silje Bakken Jørgensen, Jacqui Reilly, Oliver Kacelnik
Journal: Eurosurveillance (2023)

BackgroundGreat efforts have been made to minimise spread and prevent outbreaks of COVID-19 in hospitals. However, there is uncertainty in identifying nosocomial vs community-acquired infections. To minimise risks and evaluate measures, timely data on infection risk in healthcare institutions are required.AimsTo design an automated nationwide surveillance system for nosocomial COVID-19 using existing data to analyse the impact of community infection rates on nosocomial infections, to explore how changes in case definitions influence incidence and to identify patients and wards at highest risk and effects of SARS-CoV-2 variants.MethodsWe used data from the Norwegian real-time emergency preparedness register (Beredt C19), which includes all patients nationwide admitted to Norwegian hospitals between March 2020 and March 2022 with a positive SARS-CoV-2 PCR test during their hospital stay or within 7 days post-discharge. COVID-19 cases were assigned to categories depending on the time between admission and testing.ResultsInfection rates for definite/probable nosocomial COVID-19 increased from 0.081% in year 1 to 0.50% in year 2 in hospital admissions 7 days or longer. Varying the definitions resulted in large changes in registered nosocomial infections. Infection rates were similar across different ward types. By 2022, 58% of patients with a definite/probable nosocomial infection had received three vaccine doses.ConclusionAutomated national surveillance for nosocomial COVID-19 is possible based on existing data sources. Beredt C19 provided detailed information with only 5% missing data on hospitals/wards. Epidemiological definitions are possible to standardise, enabling easier comparison between regions and countries.
Prevalence and Clinicopathologic Characteristics of Hypercalcemia in Patients With Cholangiocarcinoma
Authors: Eirini Konstantinidou, Jordan R. Maurer, Stephanie L. Reyes, Islam Baiev, Jennifer R. Stanton, Ryan D. Nipp, Lipika Goyal
Journal: JAMA Oncology (2023)

This cohort study investigates clinicopathologic and prognostic associations of hypercalcemia in patients with intrahepatic or extrahepatic cholangiocarcinoma.
<i>Clostridioides difficile</i> aggravates dextran sulfate solution (DSS)-induced colitis by shaping the gut microbiota and promoting neutrophil recruitment
Authors: Danfeng Dong, Tongxuan Su, Wei Chen, Daosheng Wang, YiLun Xue, Qiuya Lu, Cen Jiang, Qi Ni, Enqiang Mao, Yibing Peng
Journal: Gut Microbes (2023)

Clostridioides difficile is a pathogen contributing to increased morbidity and mortality of patients with inflammatory bowel disease (IBD). To determine how C. difficile affects the severity of colitis, we constructed a dextran sulfate solution-induced colitis model challenged with C. difficile. Without antibiotic administration, C. difficile led to transient colonization in mice with colitis, but still significantly enhanced disease severity as assessed by weight loss, histopathological damages, and inflammatory cytokine concentrations. Because this effect is independent of toxin production as shown by infection with a non-toxigenic strain, we focused on changes in the gut microbiota. The microbiota altered by C.difficile, featured with reduced proportions of g_Prevotellaceae_UCG-001 and g_Muribaculaceae, were confirmed to contribute to disease severity in colitis mice via fecal microbiota transplantations. The inflamed colon showed neutrophil accumulation by flow cytometric analysis and myeloperoxidase immunochemical staining. There was enrichment of upregulated genes in leukocyte chemotaxis or migration as shown by RNA sequencing analysis. The isolated neutrophils from C. difficile-infected mice with colitis showed a robust migratory ability and had enhanced expression of cytokines and chemokines. We observed a detrimental role of neutrophils in the progress of disease by hindering neutrophil recruitment with the CXCR2 inhibitor SB225002. Furthermore, neutrophil recruitment appeared to be regulated by interleukin (IL)-1β, as inhibition of IL-1β production by MCC950 markedly ameliorated inflammation with decreased neutrophil accumulation and neutrophil-derived chemokine expression. In conclusion, our study provides information on the complicated interaction between microbiota and immune responses in C. difficile-induced inflammation in mice with colitis. Our findings could help determine potential therapeutic targets for patients with IBD concurrent with C. difficile infection.
Bioorthogonal nanozymes for breast cancer imaging and therapy
Authors: Xianzhi Zhang, Yuanchang Liu, Jeerapat Doungchawee, Laura J. Castellanos-García, Kristen N. Sikora, Taewon Jeon, Ritabrita Goswami, Stefano Fedeli, Aarohi Gupta, Rui Huang, Cristina-Maria Hirschbiegel, Roberto Cao-Milán, Prabin K.D. Majhi, Yagiz Anil Cicek, Liang Liu, D. Joseph Jerry, Richard W. Vachet, Vincent M. Rotello
Journal: Journal of Controlled Release (2023)
<i>E. coli</i> Common pili promote the fitness and virulence of a hybrid aEPEC/ExPEC strain within diverse host environments
Authors: Danielle D. Munhoz, Amanda C. Richards, Fernanda F. Santos, Matthew A. Mulvey, Roxane M. F Piazza
Journal: Gut Microbes (2023)

Pathogenic subsets of Escherichia coli include diarrheagenic (DEC) strains that cause disease within the gut and extraintestinal pathogenic E. coli (ExPEC) strains that are linked with urinary tract infections, bacteremia, and other infections outside of intestinal tract. Among DEC strains is an emergent pathotype known as atypical enteropathogenic E. coli (aEPEC), which can cause severe diarrhea. Recent sequencing efforts revealed that some E. coli strains possess genetic features that are characteristic of both DEC and ExPEC isolates. BA1250 is a newly reclassified hybrid strain with characteristics of aEPEC and ExPEC. This strain was isolated from a child with diarrhea, but its genetic features indicate that it might have the capacity to cause disease at extraintestinal sites. The spectrum of adhesins encoded by hybrid strains like BA1250 are expected to be especially important in facilitating colonization of diverse niches. E. coli common pilus (ECP) is an adhesin expressed by many E. coli pathogens, but how it impacts hybrid strains has not been ascertained. Here, using zebrafish larvae as surrogate hosts to model both gut colonization and extraintestinal infections, we found that ECP can act as a multi-niche colonization and virulence factor for BA1250. Furthermore, our results indicate that ECP-related changes in activation of envelope stress response pathways may alter the fitness of BA1250. Using an in silico approach, we also delineated the broader repertoire of adhesins that are encoded by BA1250, and provide evidence that the expression of at least a few of these varies in the absence of functional ECP.
Recommendations for Use of Video Directly Observed Therapy During Tuberculosis Treatment — United States, 2023
Authors: Joan M. Mangan, Rachel S. Woodruff, Carla A. Winston, Scott A. Nabity, Maryam B. Haddad, Meredith G. Dixon, Farah M. Parvez, Carissa Sera-Josef, LaTweika A. T. Salmon-Trejo, Chee Kin Lam
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

U.S. clinical practice guidelines recommend directly observed therapy (DOT) as the standard of care for tuberculosis (TB) treatment (1). DOT, during which a health care worker observes a patient ingesting the TB medications, has typically been conducted in person. Video DOT (vDOT) uses video-enabled devices to facilitate remote interactions between patients and health care workers to promote medication adherence and clinical monitoring. Published systematic reviews, a published meta-analysis, and a literature search through 2022 demonstrate that vDOT is associated with a higher proportion of medication doses being observed and similar proportions of cases with treatment completion and microbiologic resolution when compared with in-person DOT (2-5). Based on this evidence, CDC has updated the recommendation for DOT during TB treatment to include vDOT as an equivalent alternative to in-person DOT. vDOT can assist health department TB programs meet the U.S. standard of care for patients undergoing TB treatment, while using resources efficiently.
Ending tuberculosis in Europe - resetting the course in the post-COVID-19 era
Authors: Andrea Ammon, Hans Kluge
Journal: Eurosurveillance (2023)

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Retaining Patients with Drug-Resistant Tuberculosis on Treatment During the COVID-19 Pandemic — Dharavi, Mumbai, India, 2020–2022
Authors: Mangala D. Gomare, Sampada Bhide, Rajesh Deshmukh, Satish Kaipilyawar, Varsha Puri, Patrick K. Moonan, Dilip K. Khetade, Melissa Nyendak, Vijay Yeldandi, Jonathan P. Smith, James L. Tobias, Anand Date, Rajendra Joshi, Ravinder Kumar, Christine S. Ho
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Mumbai, India's second largest city, has one of the highest prevalences of drug-resistant tuberculosis* (DRTB) in the world.Treatment for DRTB takes longer and is more complicated than treatment for drug-susceptible tuberculosis (TB).Approximately 300 persons receive a new DRTB diagnosis each year in Mumbai's Dharavi slum † ; historically, fewer than one half of these patients complete DRTB treatment.As nationwide restrictions to mitigate the COVID-19 pandemic were implemented, a program to facilitate uninterrupted DRTB care for patients receiving treatment was also implemented.A comprehensive tool and risk assessment provided support to DRTB patients and linked those who relocated outside of Dharavi during the pandemic to DRTB care at their destination.During May 2020-September 2022, a total of 973 persons received DRTB treatment in Dharavi, including 255 (26%) who relocated during treatment.Overall, 25 (3%) DRTB patients were lost to follow-up, a rate substantially lower than the rate before the pandemic (18%).Proactive planning and implementation of simple tools retained patients on treatment during periods of travel restrictions and relocations, improving programmatic outcomes.This approach might aid public health programs serving migrant populations or patients receiving treatment for DRTB during public health emergencies.Mumbai, the capital of the state of Maharashtra, is India's second most populous city.Within Mumbai, the Dharavi slum is the largest slum in Asia and one of the most densely populated areas in the world (1 million persons in 0.8 square miles [approximately 2.1 sq km]) and is a temporary home to persons seeking informal employment from across India.§ In 2019, Dharavi reported 265 DRTB patients, one of the highest concentrations of DRTB patients in the world; however, fewer than one half successfully finished treatment ¶ (1,2).Low DRTB treatment completion is likely the consequence of the * A Mycobacterium tuberculosis isolate that is resistant to isoniazid or rifampin; resistance to additional TB medications can also be present.† Defined as "a compact settlement of at least 20 households with a collection of poorly built tenements, mostly of temporary nature, crowded together usually with inadequate sanitary and drinking water facilities in unhygienic conditions."https://mohua.gov.
Analysis of Resident and Attending Physician End-of-Rotation Changeover Days and Association With Patient Length of Stay
Authors: Fizza Manzoor, Vaakesan Sundrelingam, Surain B. Roberts, Michael Fralick, Janice L. Kwan, Terence Tang, Adina S. Weinerman, Shail Rawal, Jessica J. Liu, Donald A. Redelmeier, Amol A. Verma, Fahad Razak, Lauren Lapointe-Shaw
Journal: JAMA Network Open (2023)

Importance End-of-rotation resident physician changeover is a key part of postgraduate training but could lead to discontinuity in patient care. Objective To test whether patients exposed to end-of-rotation resident changeover have longer hospital stays and whether this association is mitigated by separating resident and attending changeover days. Design, Setting, and Participants This retrospective cohort analysis included adult patients admitted to general internal medicine. The changeover day was the same day (first Monday of month) for both resident and attending physicians until June 30, 2013 (preseparation period), and then intentionally staggered by 1 or more days after July 1, 2013 (postseparation period). This was a multicenter analysis at 4 teaching hospitals in Ontario, Canada, from July 1, 2010, to June 30, 2019. Data analysis was conducted from July 2022 to January 2023. Exposures Patients were classified as changeover patients if the first Monday was a resident changeover day and as control patients if the first Monday was not a resident changeover day. Main Outcomes and Measures The primary outcome was length of hospital stay. Secondary outcomes were transfer to critical care, in-hospital death, and rate of discharge per 100 patients on the index day. Results Of 95 282 patients. 22 773 (24%; mean [SD] age, 67.8 [18.8] years; 11 156 [49%] female patients) were exposed to resident changeover, and 72 509 (76%; mean [SD] age, 67.8 [18.7] years; 35 293 [49%] female patients) were not exposed to resident changeover. Exposure to resident changeover day was associated with a slightly longer hospital stay compared with control days (0.20 [95% CI, 0.09-0.30] days; P &amp;amp;lt; .001) and decreased relative risk of patient discharge on the index day (relative risk, 0.92; 95% CI, 0.86-1.00; P = .047). These associations were similar in the preseparation and postseparation periods. Resident changeover was not associated with an increased risk of transfer to critical care or in-hospital death. Conclusions and Relevance In this study, a small positive association between exposure to resident physician changeover and length of hospital stay as well as reduced rate of discharge was found. These findings suggest that separating changeover days for resident and attending physicians may not significantly change these associations.
Prevalence and Characteristics of Autism Spectrum Disorder Among Children Aged 8 Years — Autism and Developmental Disabilities Monitoring Network, 11 Sites, United States, 2020
Authors: Matthew J. Maenner, Zachary Warren, Ashley Robinson Williams, Esther Amoakohene, Amanda V. Bakian, Deborah A. Bilder, Maureen S. Durkin, Robert T. Fitzgerald, Sarah M. Furnier, Michelle M. Hughes, Christine M. Ladd-Acosta, Dedria McArthur, Elise T. Pas, Angelica Salinas, Alison Vehorn, Susan Williams, Amy Esler, Andrea Grzybowski, Jennifer Hall-Lande, Ruby H.N. Nguyen, Karen Pierce, Walter Zahorodny, Allison Hudson, Libby Hallas, Kristen Clancy Mancilla, Mary Patrick, Josephine Shenouda, Kate Sidwell, Monica DiRienzo, Johanna Gutierrez, Margaret H. Spivey, Maya Lopez, Sydney Pettygrove, Yvette D. Schwenk, Anita Washington, Kelly A. Shaw
Journal: MMWR Surveillance Summaries (2023)

Autism spectrum disorder (ASD).
Association of Antibiotic Receipt With Survival Among Patients With Metastatic Pancreatic Ductal Adenocarcinoma Receiving Chemotherapy
Authors: Daniel J. Fulop, Haley M. Zylberberg, Y. Linda Wu, Anne Aronson, Arielle J. Labiner, Juan Wisnivesky, Deirdre J. Cohen, Keith M. Sigel, Aimee L. Lucas
Journal: JAMA Network Open (2023)

Importance The prognosis for patients with metastatic pancreatic ductal adenocarcinoma (PDAC) is dismal, due in part to chemoresistance. Bacteria-mediated mechanisms of chemoresistance suggest a potential role for antibiotics in modulating response to chemotherapy. Objective To evaluate whether use of peritreatment antibiotics is associated with survival among patients with metastatic PDAC treated with first-line gemcitabine or fluorouracil chemotherapy. Design, Setting, and Participants Using the population-based Surveillance, Epidemiology, and End Results–Medicare linked database, this retrospective cohort study analyzed data for patients diagnosed with PDAC between January 1, 2007, and December 31, 2017. Data analysis was conducted between September 1, 2021, and January 15, 2023. The population-based sample included 3850 patients with primary metastatic PDAC treated with first-line gemcitabine or fluorouracil chemotherapy. Patients who received antibiotics were matched based on propensity scores to patients who did not receive antibiotics. Exposures Receipt of 5 or more days of oral antibiotics or 1 injectable antibiotic in the month before or after beginning first-line chemotherapy. Main Outcomes and Measures Overall survival and cancer-specific survival. The end of follow-up was December 31, 2019, for overall survival and December 31, 2018, for cancer-specific survival. Results Of the 3850 patients treated with first-line gemcitabine (3150 [81.8%]) or fluorouracil (700 [18.2%]), 2178 (56.6%) received antibiotics. The mean (SD) age at diagnosis was 74.2 (5.8) years and patients were predominantly women (2102 [54.6%]), White (3396 [88.2%]), and from metropolitan areas (3393 [88.1%]) in the northeastern or western US (2952 [76.7%]). In total, 1672 propensity-matched pairs were analyzed. Antibiotic receipt was associated with an 11% improvement in overall survival (hazard ratio [HR], 0.89; 95% CI, 0.83-0.96; P = .003) and a 16% improvement in cancer-specific survival (HR, 0.84; 95% CI, 0.77-0.92; P &amp;amp;lt; .001) among patients treated with gemcitabine. In contrast, there was no association between antibiotic receipt and overall survival (HR, 1.08; 95% CI, 0.90-1.29; P = .41) or cancer-specific survival (HR, 1.12; 95% CI, 0.90-1.36; P = .29) among patients treated with fluorouracil. In a subgroup of gemcitabine-treated patients who received antibiotics, nonpenicillin β-lactams were associated with an 11% survival benefit (HR, 0.89; 95% CI, 0.81-0.97; P = .01). Conclusions and Relevance In this cohort study, receipt of perichemotherapy antibiotics was associated with improved survival among patients treated with gemcitabine, but not fluorouracil, suggesting that antibiotics may modulate bacteria-mediated gemcitabine resistance and have the potential to improve PDAC outcomes.
Enterohemorrhagic <i>Escherichia coli</i> responds to gut microbiota metabolites by altering metabolism and activating stress responses
Authors: Stefanie L. Vogt, Antonio Serapio-Palacios, Sarah E. Woodward, Andrew S. Santos, Stefan P.W. de Vries, Michelle C. Daigneault, Lisa V. Brandmeier, Andrew J. Grant, Duncan J. Maskell, Emma Allen-Vercoe, B. Brett Finlay
Journal: Gut Microbes (2023)

Enterohemorrhagic Escherichia coli (EHEC) is a major cause of severe bloody diarrhea, with potentially lethal complications, such as hemolytic uremic syndrome. In humans, EHEC colonizes the colon, which is also home to a diverse community of trillions of microbes known as the gut microbiota. Although these microbes and the metabolites that they produce represent an important component of EHEC's ecological niche, little is known about how EHEC senses and responds to the presence of gut microbiota metabolites. In this study, we used a combined RNA-Seq and Tn-Seq approach to characterize EHEC's response to metabolites from an in vitro culture of 33 human gut microbiota isolates (MET-1), previously demonstrated to effectively resolve recurrent Clostridioides difficile infection in human patients. Collectively, the results revealed that EHEC adjusts to growth in the presence of microbiota metabolites in two major ways: by altering its metabolism and by activating stress responses. Metabolic adaptations to the presence of microbiota metabolites included increased expression of systems for maintaining redox balance and decreased expression of biotin biosynthesis genes, reflecting the high levels of biotin released by the microbiota into the culture medium. In addition, numerous genes related to envelope and oxidative stress responses (including cpxP, spy, soxS, yhcN, and bhsA) were upregulated during EHEC growth in a medium containing microbiota metabolites. Together, these results provide insight into the molecular mechanisms by which pathogens adapt to the presence of competing microbes in the host environment, which ultimately may enable the development of therapies to enhance colonization resistance and prevent infection.
Active tuberculosis screening among the displaced population fleeing Ukraine, France, February to October 2022
Authors: Jean-Paul Guthmann, Philippe Fraisse, Isabelle Bonnet, Jérôme Robert
Journal: Eurosurveillance (2023)

Persons fleeing Ukraine since February 2022 have potentially higher risk of tuberculosis (TB) vs all European Union countries. Interest of active TB screening among this population is debated and not widely adopted. In this screening intervention by a network of TB centres in France, the number needed to screen (NNS) was 862 to find one case. This experience shows that this strategy may be relevant for TB control in situations of massive displacement, similar to that following the Russian invasion.
Sequencing Identifies Relapse-Prone AML Patients
Journal: Cancer Discovery (2023)

For patients with acute myeloid leukemia, DNA sequencing before stem cell transplant can predict the chances of relapse, research shows. Scientists found that NPM1 alterations and/or FLT3 internal tandem duplications that persist after treatment and prior to a stem cell transplant were better predictors of relapse than flow cytometry.